Queen Bee is voiced by Marina Sirtis, who voiced Demona. Both characters share similar physical traits: Queen Bee dons a veil around her shoulders, which mirrors Demona's wings when furled; she also wears a gold armband similar to the one that Demona used on her left arm, and a golden diadem that resembles Demona's headpiece; and both wear golden earrings.
Vandal Savage has three facial scars that bear a striking resemblance to those that Demona gave to Gillecomgain, which later came to be the signature mark of the Hunters. However, Savage's scars are not an intentional reference to the Hunters. They were part of his original design by Phil Bourassa.
Various villains (mostly those who work for the Light) exhibit a Xanatos-like perspective about loss: every time they are thwarted by the Team they never acknowledge defeat, but rather perceive some sort of victory from the events in a very calm and nonchalant demeanor:
Red Tornado says that he is not sure if the Team's words are accurate, but they may be true. This is reminiscent of King Arthur's line "all things are true... few things are accurate" in the Gargoyles comic "Rock & Roll".
One of Zatanna's spells ("Erif nrub, nordluac elbbub") translates into "Fire burn, cauldron bubble", which is a quote from William Shakespeare Macbeth (Act Four, Scene One). This line was also used in the recreated scene of the play in the episode "City of Stone" Part Three.
The main plot of this episode turned out to be an over-elaborate ploy contrived by the antagonists in order to divert attentions and secure an unrelated goal. This was also done in "Leader of the Pack", "Metamorphosis", "Legion" and "High Noon".
Klarion says "Team work is so overrated." Thailog said the same thing in "Sanctuary".
When Superboy breaks free from the illusion, he shouts, "None of this is real". This mirrors Goliath's scream "None of you are real" when he breaks free from his hallucinations in "Shadows of the Past".
Harm is voiced by Ben Diskin who also voiced Venom. Both characters exhibit idiosyncratic speech patterns: Venom spoke in the first-person plural to refer to himself ("we"), while Harm refers to himself in the third-person singular and uses the impersonal pronoun to refer to others ("it", "they" and a pluralized "its"). Moreover, both are psychotic and both have bound and gagged a character voiced by Lacey Chabert.
Deathstroke's line "I hate to see any poor animal suffer" is very similar to what Shocker says in "Accomplices": "Never did like to see a poor, dumb animal suffer."
Young Justice uses timestamps to "ground the show in the moment and allow fans to get how much time has passed between episodes". Greg Weisman explained that and it was "the next logical step from what [he] tried to do on Spectacular Spider-Man" in which the timeline could be pinpointed by seasonal holidays. Prior to this, Weisman had first used timestamps on three issues of the Gargoyles comics by SLG: "The Rock", "Rock & Roll" and "Rock of Ages". The first two of those issues did not include locations, however, the third did: continuing the sense of progression.